Update links from oceanparcels.org to parcels-code.org

README.md

@@ -1,7 +1,7 @@
 ## plasticparcels
 `plasticparcels` is a python package for simulating the transport and dispersion of plastics in the ocean.
 
-The tool is based on the [`Parcels`](https://oceanparcels.org/) computational Lagrangian ocean analysis framework ([@Lange2017](http://dx.doi.org/10.5194/gmd-10-4175-2017) and [@Delandmeter2019](http://dx.doi.org/10.5194/gmd-12-3571-2019)), providing a modular and customisable collection of methods, notebooks, and tutorials for advecting virtual plastic particles with a wide range of physical properties. A peer reviewed paper describing `plasticparcels` can be found here: [![DOI](https://joss.theoj.org/papers/10.21105/joss.07094/status.svg)](https://doi.org/10.21105/joss.07094).
+The tool is based on the [`Parcels`](https://parcels-code.org/) computational Lagrangian ocean analysis framework ([@Lange2017](http://dx.doi.org/10.5194/gmd-10-4175-2017) and [@Delandmeter2019](http://dx.doi.org/10.5194/gmd-12-3571-2019)), providing a modular and customisable collection of methods, notebooks, and tutorials for advecting virtual plastic particles with a wide range of physical properties. A peer reviewed paper describing `plasticparcels` can be found here: [![DOI](https://joss.theoj.org/papers/10.21105/joss.07094/status.svg)](https://doi.org/10.21105/joss.07094).
 
 ![plasticparcels](docs/_static/plasticparcelslogo.png)
 
@@ -26,26 +26,26 @@ For downloading the wind and wave data, we recommend using the [CDS API](https:/
 
 To run most of the examples, you will need to update the data directories in the relevant settings `.json` file.
 
-Just like the `parcels` framework, `plasticparcels` can be adapted to use other hydrodynamic, biogeochemical, wave, and atmospheric models. If you require assistance, please contact us through the [`plasticparcels` discussions page](https://github.com/OceanParcels/plasticparcels/discussions).
+Just like the `parcels` framework, `plasticparcels` can be adapted to use other hydrodynamic, biogeochemical, wave, and atmospheric models. If you require assistance, please contact us through the [`plasticparcels` discussions page](https://github.com/Parcels-code/plasticparcels/discussions).
 
 ### Community contributions and support
 #### Contributing code
-We welcome contributions to `plasticparcels`, especially example workbooks and analyses for our [public examples page](https://plastic.oceanparcels.org/en/latest/examples.html). To contribute to the project, please submit a [pull request](https://github.com/OceanParcels/plasticparcels/pulls).
+We welcome contributions to `plasticparcels`, especially example workbooks and analyses for our [public examples page](https://plastic.parcels-code.org/en/latest/examples.html). To contribute to the project, please submit a [pull request](https://github.com/Parcels-code/plasticparcels/pulls).
 
 #### Requesting features and reporting issues/bugs
-If you want to request a new feature, or if you find an issue or bug in the code, please open an issue in the [`plasticparcels` issue tracker](https://github.com/OceanParcels/plasticparcels/issues).
+If you want to request a new feature, or if you find an issue or bug in the code, please open an issue in the [`plasticparcels` issue tracker](https://github.com/Parcels-code/plasticparcels/issues).
 
 #### Seeking support?
-If you would like support using `plasticparcels`, or are have any questions about your `plasticparcels` simulations, please start a discussion in the [`plasticparcels` discussion page](https://github.com/OceanParcels/plasticparcels/discussions).
+If you would like support using `plasticparcels`, or are have any questions about your `plasticparcels` simulations, please start a discussion in the [`plasticparcels` discussion page](https://github.com/Parcels-code/plasticparcels/discussions).
 
 
 
 
 ### Further information
-For more information and documentation, see the [plasticparcels documentation](https://plastic.oceanparcels.org/).
+For more information and documentation, see the [plasticparcels documentation](https://plastic.parcels-code.org/).
 
 [![DOI](https://joss.theoj.org/papers/10.21105/joss.07094/status.svg)](https://doi.org/10.21105/joss.07094)
-[![unit-tests](https://github.com/OceanParcels/plasticparcels/actions/workflows/unit_tests.yml/badge.svg)](https://github.com/OceanParcels/plasticparcels/actions/workflows/unit_tests.yml)
+[![unit-tests](https://github.com/Parcels-code/plasticparcels/actions/workflows/unit_tests.yml/badge.svg)](https://github.com/Parcels-code/plasticparcels/actions/workflows/unit_tests.yml)
 [![Anaconda-release](https://anaconda.org/conda-forge/plasticparcels/badges/version.svg)](https://anaconda.org/conda-forge/plasticparcels/)
 [![Anaconda-date](https://anaconda.org/conda-forge/plasticparcels/badges/latest_release_date.svg)](https://anaconda.org/conda-forge/plasticparcels/)
 [![Zenodo](https://zenodo.org/badge/DOI/10.5281/zenodo.11388383.svg)](https://doi.org/10.5281/zenodo.11388383)

docs/conf.py

@@ -17,8 +17,8 @@
 import plasticparcels
 
 project = 'plasticparcels'
-copyright = f'{datetime.datetime.now().year}, The OceanParcels Team'
-author = 'The OceanParcels Team'
+copyright = f'{datetime.datetime.now().year}, The Parcels Team'
+author = 'The Parcels Team'
 
 # -- General configuration ---------------------------------------------------
 # https://www.sphinx-doc.org/en/master/usage/configuration.html#general-configuration
@@ -56,7 +56,7 @@
         "image_dark": "plasticparcelslogo_inverted.png",
     },
     # "use_edit_page_button": True,
-    "github_url": "https://github.com/OceanParcels/plasticparcels",
+    "github_url": "https://github.com/Parcels-code/plasticparcels",
     "icon_links": [
         {
             "name": "Conda Forge",
@@ -144,9 +144,9 @@ def linkcode_resolve(domain, info):
     fn = os.path.relpath(fn, start=os.path.dirname(plasticparcels.__file__))
 
     if is_non_standard_version(plasticparcels.__version__):
-        return f"https://github.com/OceanParcels/plasticparcels/blob/main/plasticparcels/{fn}{linespec}"
+        return f"https://github.com/Parcels-code/plasticparcels/blob/main/plasticparcels/{fn}{linespec}"
     else:
         return (
-            f"https://github.com/OceanParcels/plasticparcels/blob/"
+            f"https://github.com/Parcels-code/plasticparcels/blob/"
             f"v{plasticparcels.__version__}/plasticparcels/{fn}{linespec}"
         )

docs/examples/README.md

@@ -1,3 +1,3 @@
 # Examples
 
-Up-to-date documentation on the `plasticparcels` examples can be found [here](https://plastic.oceanparcels.org/en/latest/examples.html).
+Up-to-date documentation on the `plasticparcels` examples can be found [here](https://plastic.parcels-code.org/en/latest/examples.html).

docs/examples/example_Croatian_fisheries.ipynb

@@ -5,10 +5,10 @@
    "metadata": {},
    "source": [
     "# Sensitivity of biofouling parameters - Plastic pollution from Croatian fishing vessels\n",
-    "In this example, we will use `plasticparcels` to run a basic simulation of microplastic pollution emitted from Croatian registered fishing vessels. We will use the [Open-sea fishing-related plastic emissions dataset](https://plastic.oceanparcels.org/en/latest/initialisationmaps.html#open-sea-fishing-related-plastic-emissions) to release virtual particles in ocean model grid cells, using the 3D velocity fields to advect the particles. We also include the effects of biofouling and Stokes drift on the particles. We will run two simulations, one with the default biofouling parameters, and another where we vary some of the biofouling parameters.\n",
+    "In this example, we will use `plasticparcels` to run a basic simulation of microplastic pollution emitted from Croatian registered fishing vessels. We will use the [Open-sea fishing-related plastic emissions dataset](https://plastic.parcels-code.org/en/latest/initialisationmaps.html#open-sea-fishing-related-plastic-emissions) to release virtual particles in ocean model grid cells, using the 3D velocity fields to advect the particles. We also include the effects of biofouling and Stokes drift on the particles. We will run two simulations, one with the default biofouling parameters, and another where we vary some of the biofouling parameters.\n",
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "<b>Note: </b> To run this example you will need to download the hydrodynamic, physical, and biogeochemical model data described [here](https://plastic.oceanparcels.org/en/latest/index.html#required-data).\n",
+    "<b>Note: </b> To run this example you will need to download the hydrodynamic, physical, and biogeochemical model data described [here](https://plastic.parcels-code.org/en/latest/index.html#required-data).\n",
     "\n",
     "</div>"
    ]
@@ -84,7 +84,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Next, we define our release settings and plastic particle type. In this example we will use the `fisheries` release type (see [here](https://plastic.oceanparcels.org/en/latest/initialisationmaps.html) for more detail), selecting only release locations related to Croatian fishing vessels. We will simulate the pathways of plastic particles that are 0.1mm in diameter. We will give the plastic particles a denisity of 1028 kg/m<sup>3</sup>."
+    "Next, we define our release settings and plastic particle type. In this example we will use the `fisheries` release type (see [here](https://plastic.parcels-code.org/en/latest/initialisationmaps.html) for more detail), selecting only release locations related to Croatian fishing vessels. We will simulate the pathways of plastic particles that are 0.1mm in diameter. We will give the plastic particles a denisity of 1028 kg/m<sup>3</sup>."
    ]
   },
   {
@@ -119,7 +119,7 @@
    "metadata": {},
    "source": [
     "## Create a `FieldSet`, `ParticleSet` and `Kernel` list\n",
-    "Here we create the necessary `Parcels` objects to run our simulation. The `FieldSet` contains all the hydrodynamic, wind, and wave data required for our simulation. The `ParticleSet` is a set of particles initialised along the Greek coastline, and the `Kernel` list is a list of kernels that will be applied to these particles. A useful overview of these `Parcels` objects can be found [here](https://docs.oceanparcels.org/en/latest/examples/tutorial_parcels_structure.html)."
+    "Here we create the necessary `Parcels` objects to run our simulation. The `FieldSet` contains all the hydrodynamic, wind, and wave data required for our simulation. The `ParticleSet` is a set of particles initialised along the Greek coastline, and the `Kernel` list is a list of kernels that will be applied to these particles. A useful overview of these `Parcels` objects can be found [here](https://docs.parcels-code.org/en/latest/examples/tutorial_parcels_structure.html)."
    ]
   },
   {
@@ -206,7 +206,7 @@
    "metadata": {},
    "source": [
     "## Plot the trajectories\n",
-    "Finally, we produce a simple 'spaghetti' plot of the trajectories to visualise their pathways. To understand how to work with `PlasticParcels` output, please see the `Parcels` tutorial [here](https://docs.oceanparcels.org/en/latest/examples/tutorial_output.html)."
+    "Finally, we produce a simple 'spaghetti' plot of the trajectories to visualise their pathways. To understand how to work with `PlasticParcels` output, please see the `Parcels` tutorial [here](https://docs.parcels-code.org/en/latest/examples/tutorial_output.html)."
    ]
   },
   {

docs/examples/example_Greece_coast.ipynb

@@ -5,10 +5,10 @@
    "metadata": {},
    "source": [
     "# The pathways and fate of existing plastic pollution along Greek coastlines\n",
-    "In this example, we will use `plasticparcels` to run a basic simulation of microplastic pollution along the Greek coastline. We will use the [Current global ocean plastic concentrations dataset](https://plastic.oceanparcels.org/en/latest/initialisationmaps.html) to release virtual particles in coastal model grid cells, using the 2D surface velocity fields to advect the particles. We also include the effects of Stokes drift and wind-induced drift on the particles, but neglect any vertical motion (along with any biofouling, or vertical mixing).\n",
+    "In this example, we will use `plasticparcels` to run a basic simulation of microplastic pollution along the Greek coastline. We will use the [Current global ocean plastic concentrations dataset](https://plastic.parcels-code.org/en/latest/initialisationmaps.html) to release virtual particles in coastal model grid cells, using the 2D surface velocity fields to advect the particles. We also include the effects of Stokes drift and wind-induced drift on the particles, but neglect any vertical motion (along with any biofouling, or vertical mixing).\n",
     "<div class=\"alert alert-block alert-info\">\n",
     "\n",
-    "<b>Note: </b> To run this example you will need to download the hydrodynamic, physical, and biogeochemical model data described [here](https://plastic.oceanparcels.org/en/latest/index.html#required-data).\n",
+    "<b>Note: </b> To run this example you will need to download the hydrodynamic, physical, and biogeochemical model data described [here](https://plastic.parcels-code.org/en/latest/index.html#required-data).\n",
     "\n",
     "</div>"
    ]
@@ -84,7 +84,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "Next, we define our release settings and plastic particle type. In this example we will use the `global_concentrations` release type, and set `concentration_type = Beach` (see [here](https://plastic.oceanparcels.org/en/latest/initialisationmaps.html) for more detail), selecting only release locations along the Greek coastline. We will simulate the pathways of plastic particles that at 0.1mm, and will apply a wind coefficient of 1%. We give the plastic particles a denisity of 1030 kg/m<sup>3</sup>, however, since this is an ocean-surface only simulation, this parameter will have no impact on our simulation."
+    "Next, we define our release settings and plastic particle type. In this example we will use the `global_concentrations` release type, and set `concentration_type = Beach` (see [here](https://plastic.parcels-code.org/en/latest/initialisationmaps.html) for more detail), selecting only release locations along the Greek coastline. We will simulate the pathways of plastic particles that at 0.1mm, and will apply a wind coefficient of 1%. We give the plastic particles a denisity of 1030 kg/m<sup>3</sup>, however, since this is an ocean-surface only simulation, this parameter will have no impact on our simulation."
    ]
   },
   {
@@ -120,7 +120,7 @@
    "metadata": {},
    "source": [
     "## Create a `FieldSet`, `ParticleSet` and `Kernel` list\n",
-    "Here we create the necessary `Parcels` objects to run our simulation. The `FieldSet` contains all the hydrodynamic, wind, and wave data required for our simulation. The `ParticleSet` is a set of particles initialised along the Greek coastline, and the `Kernel` list is a list of kernels that will be applied to these particles. A useful overview of these `Parcels` objects can be found [here](https://docs.oceanparcels.org/en/latest/examples/tutorial_parcels_structure.html)."
+    "Here we create the necessary `Parcels` objects to run our simulation. The `FieldSet` contains all the hydrodynamic, wind, and wave data required for our simulation. The `ParticleSet` is a set of particles initialised along the Greek coastline, and the `Kernel` list is a list of kernels that will be applied to these particles. A useful overview of these `Parcels` objects can be found [here](https://docs.parcels-code.org/en/latest/examples/tutorial_parcels_structure.html)."
    ]
   },
   {
@@ -215,7 +215,7 @@
    "metadata": {},
    "source": [
     "## Plot the trajectories\n",
-    "Finally, we produce a simple 'spaghetti' plot of the trajectories to visualise their pathways. To understand how to work with `PlasticParcels` output, please see the `Parcels` tutorial [here](https://docs.oceanparcels.org/en/latest/examples/tutorial_output.html)."
+    "Finally, we produce a simple 'spaghetti' plot of the trajectories to visualise their pathways. To understand how to work with `PlasticParcels` output, please see the `Parcels` tutorial [here](https://docs.parcels-code.org/en/latest/examples/tutorial_output.html)."
    ]
   },
   {